Literature DB >> 24838331

Clinical validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing.

Ming-Tseh Lin1, Stacy L Mosier1, Michele Thiess1, Katie F Beierl1, Marija Debeljak1, Li-Hui Tseng2, Guoli Chen1, Srinivasan Yegnasubramanian3, Hao Ho1, Leslie Cope3, Sarah J Wheelan3, Christopher D Gocke4, James R Eshleman5.   

Abstract

OBJECTIVES: To validate next-generation sequencing (NGS) technology for clinical diagnosis and to determine appropriate read depth.
METHODS: We validated the KRAS, BRAF, and EGFR genes within the Ion AmpliSeq Cancer Hotspot Panel using the Ion Torrent Personal Genome Machine (Life Technologies, Carlsbad, CA).
RESULTS: We developed a statistical model to determine the read depth needed for a given percent tumor cellularity and number of functional genomes. Bottlenecking can result from too few input genomes. By using 16 formalin-fixed, paraffin-embedded (FFPE) cancer-free specimens and 118 cancer specimens with known mutation status, we validated the six traditional analytic performance characteristics recommended by the Next-Generation Sequencing: Standardization of Clinical Testing Working Group. Baseline noise is consistent with spontaneous and FFPE-induced C:G→T:A deamination mutations.
CONCLUSIONS: Redundant bioinformatic pipelines are essential, since a single analysis pipeline gave false-negative and false-positive results. NGS is sufficiently robust for the clinical detection of gene mutations, with attention to potential artifacts. Copyright© by the American Society for Clinical Pathology.

Entities:  

Keywords:  BRAF; Deamination; EGFR; KRAS; Next-generation sequencing; Read depth; Validation

Mesh：

Substances：

Year:  2014        PMID： 24838331      PMCID： PMC4332779          DOI： 10.1309/AJCPMWGWGO34EGOD

Source DB:  PubMed          Journal:  Am J Clin Pathol        ISSN： 0002-9173            Impact factor:   2.493


  58 in total

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Journal:  Cancer Discov       Date:  2011-12-29       Impact factor: 39.397

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Journal:  Genet Med       Date:  2011-11       Impact factor: 8.822

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  60 in total

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